[pymvpa] Problem installing on Mac OS X #shogun26vs25 #deprecation warning

[Michael Hanke]

Hi Christian,


I'm glad you managed to get it running. Thanks a lot for reporting how
you did it -- I'm sure other MacOS users will appreciate that!

Michael


On Mon, Dec 14, 2009 at 04:06:56PM +0100, Christian Fiebach wrote:
> Dear all,
> 
> a brief update, just in case this might help others:
> 
> I managed to install py25-pymvpa under leopard finally.
> 
> 
> #shogun:
> It appears that the current version of shogun in MacPorts (i.e.,
> 0.9) is dependent on
> python26, which caused MacPorts to additionally install python26
> (see earlier mail in the
> thread). This can be suppressed by installing shogun in the
> following way:
> 
> sudo port -v install shogun +no_python26 +python25
> 
> which makes installation of py25-pymvpa (sudo port install py25-
> pymvpa) possible.
> 
> 
> #Deprecation warning: Some problems seem to persist:
> 
> >>> from mvpa.suite import *
> /opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/
> python2.5/site-packages/matplotlib/numerix/__init__.py:18:
> DeprecationWarning:
> **********************************************************
> matplotlib.numerix and all its subpackages are deprecated.
> They will be removed soon.  Please use numpy instead.
> **********************************************************
> 
>   warnings.warn(msg, DeprecationWarning)
> 
> 
> Best, Christian
> 
> 
> Am 10.12.2009 um 17:13 schrieb Christian Fiebach:
> 
> >Thanks Anna,
> >
> >installing as you suggested fully using py26 worked, with your
> >commands given below. Thanks!!!
> >
> >However, my first steps in pyMVPA continue to be difficult:
> >
> >When I start python and try to follow the installation website or
> >the getting started manual,
> >python produces either error messages or crashes:
> >
> >From the installation web site: Deprecation Warning @ import and
> >NameError for the very first command.
> >
> >fiebach$ python
> >Python 2.6.4 (r264:75706, Dec  8 2009, 01:05:52)
> >[GCC 4.2.1 (Apple Inc. build 5646) (dot 1)] on darwin
> >Type "help", "copyright", "credits" or "license" for more information.
> >>>> import mvpa
> >/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/
> >python2.6/site-packages/mvpa/base/verbosity.py:19:
> >DeprecationWarning: the sets module is deprecated
> >  from sets import Set
> >>>> attr = SampleAttributes(os.path.join(pymvpa_dataroot,
> >'attributes.txt'))
> >Traceback (most recent call last):
> >  File "<stdin>", line 1, in <module>
> >NameError: name 'SampleAttributes' is not defined
> >>>>
> >
> >
> >From the Getting Started section of the Manual: Deprecatin error
> >and python crash
> >
> >fiebach$ python
> >Python 2.6.4 (r264:75706, Dec  8 2009, 01:05:52)
> >[GCC 4.2.1 (Apple Inc. build 5646) (dot 1)] on darwin
> >Type "help", "copyright", "credits" or "license" for more information.
> >>>> from mvpa.suite import *
> >/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/
> >python2.6/site-packages/mvpa/base/verbosity.py:19:
> >DeprecationWarning: the sets module is deprecated
> >  from sets import Set
> >Python(673) malloc: *** error for object 0x7fff70e8b500: pointer
> >being freed was not allocated
> >*** set a breakpoint in malloc_error_break to debug
> >Abort trap
> >fiebach$
> >
> >
> >Just to make sure: My path seems to look fine. The export command
> >is currently in .profile,
> >not in .bash_profile as suggested in the installation section:
> >
> >fiebach$ echo $PATH
> >/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/
> >local/bin:/usr/X11/bin
> >
> >
> >
> >Unfortunately, I am just starting to use python and therefore my
> >debugging abilities
> >are not very advanced at present. I am greatful for any input you
> >can give me right
> >now!
> >
> >Thanks in advance,
> >
> >Christian
> >
> >
> >Am 08.12.2009 um 14:57 schrieb Anna Manelis:
> >
> >>Christian,
> >>I am not an expert, but I managed to install PYMVPA on my Snow
> >>Leopard by doing
> >>sudo port install py26-pil py26-numpy py26-scipy py26-ipython
> >>py26-matplotlib +cairo+latex+tkinter  py26-pyobjc2-cocoa
> >>python_select
> >>sudo python_select python26
> >>And then
> >>sudo port install py26-pymvpa +scipy +pynifti +hcluster +libsvm
> >>+matplotlib +pywavelet
> >>Although when I tried to install PYMVPA on Leopard, I
> >>encountered the same problem as you (the installation involves
> >>py26 even though I explicitly aske it to involve py25).
> >>
> >>Good luck,
> >>Anna.
> >>
> >
> >
> >
> >
> >
> >_______________________________________________
> >Pkg-ExpPsy-PyMVPA mailing list
> >Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org
> >http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-pymvpa
> 
> 
> 
> 
> -------------------------------------------------------------
> Prof. Dr. Christian Fiebach
> Dept. of Psychology, University of Heidelberg
> Hauptstr. 47-51; D-69117 Germany
> Tel.: ++49-(0)6221-547371
> http://fimlab.uni-hd.de
> -------------------------------------------------------------
> 
> 
> 
> 

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-- 
GPG key:  1024D/3144BE0F Michael Hanke
http://mih.voxindeserto.de